I am going to say the MC Hana from Wolf Children. She first popped into mind the minute the topic was offered.

I will also mention Trisha Elric from Full Metal Alchemist (specifically the Brotherhood series), and not just because she is the impetus for the Elric boys pushing the envelope of Alchemy, but because of the love she had for her sons.

I'm going to with with one of the most bad ass moms around. Balalaika from Black Lagoon,best mom out there. Sure she runs the Russian mafia but that doesn't mean she can't be a good mother to her men. After all when someone kills one of your "sons" wouldn't you go on a killing rampage finding him, then killing them slowly even if they are a killer child. Best mom ever!